Mercurial > repos > iuc > data_manager_pharokka

annotate data_manager/pharokka_db_fetcher.xml @ 0:3b3daabcc63e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
author iuc
date Thu, 20 Apr 2023 07:51:13 +0000
parents
children bba8135dc024
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
2 <tool id="pharokka_db_fetcher" name="phrokka DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
3 <macros>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
4 <import>macros.xml</import>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
5 </macros>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
6 <expand macro="biotools" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
7 <expand macro="requirements" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
8 <expand macro="version" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
9 <description>Fetches the DB required for phrokka</description>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
10 <command detect_errors="exit_code">
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
11 <![CDATA[
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
12 python '$__tool_directory__/data_manager_fetch_pharokka_db.py' --out '${out_file}' --version '${version}'
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
13 $test_data_manager
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
14 ]]>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
15 </command>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
16 <inputs>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
17 <param name="test_data_manager" type="hidden" value=""/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
18 <param argument="--version" type="text" value="v1.2.0" help="Check https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 for current version."/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
19 </inputs>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
20 <outputs>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
21 <data format="data_manager_json" name="out_file" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
22 </outputs>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
23 <tests>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
24 <test expect_num_outputs="1">
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
25 <param name="test_data_manager" value="--test"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
26 <param name="version" value="v1.2.0"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
27 <output name="out_file">
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
28 <assert_contents>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
29 <has_text text="Pharokka DB version"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
30 <has_text text="db_from_"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
31 <has_text text="pharokka_db"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
32 <has_text text="v1.2.0"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
33 </assert_contents>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
34 </output>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
35 </test>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
36 </tests>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
37 <help>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
38 </help>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
39 <expand macro="citations" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
40 <expand macro="creator" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
parents:
diff changeset
41 </tool>